19-50798138-C-A

Variant names:

• chr19-50798138-C-A
• rs4801853
• ENST00000598463.5:n.1410G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000598463.5(C19orf48P):​n.1410G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C19orf48P ENST00000598463.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404
• Publications: 42 publications found

Genes affected

C19orf48P (HGNC:):

C19orf48P (HGNC:29667): (chromosome 19 open reading frame 48, pseudogene)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20584905).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598463.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	NR_171554.1		n.1110G>T		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	NR_171555.1		n.949G>T		non_coding_transcript_exon	Exon 4 of 4
	C19orf48P	NR_171556.1		n.1454G>T		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf48P	ENST00000598463.5	TSL:1	n.1410G>T		non_coding_transcript_exon	Exon 5 of 5
	C19orf48P	ENST00000596287.7	TSL:2	n.980G>T		non_coding_transcript_exon	Exon 4 of 4
	C19orf48P	ENST00000596655.1	TSL:2	n.1262G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.71
DANN	Benign	0.77
DEOGEN2	Benign	0.025	T
Eigen	Benign	-0.91
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.067	N
LIST_S2	Benign	0.32	T
M_CAP	Benign	0.0058	T
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.40
PROVEAN	Pathogenic	-6.6	D
REVEL	Benign	0.13
Sift4G	Pathogenic	0.0	D
Polyphen		0.97	D
Vest4		0.23
MutPred		0.25		Gain of helix (P = 0.0117)
MVP		0.40
ClinPred		0.34	T
GERP RS		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.26
gMVP		0.065

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4801853; hg19: chr19-51301395;